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<!-- doxytag: class="moltk::Aligner" -->
<p>The <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> class creates macromolecule sequence alignments and structure alignments.  
 <a href="classmoltk_1_1Aligner.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a>&gt;</code></p>
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Collaboration diagram for moltk::Aligner:</div>
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<div class="center"><img src="classmoltk_1_1Aligner__coll__graph.png" border="0" usemap="#moltk_1_1Aligner_coll__map" alt="Collaboration graph"/></div>
<map name="moltk_1_1Aligner_coll__map" id="moltk_1_1Aligner_coll__map">
<area shape="rect" id="node2" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures." alt="" coords="621,71,741,97"/><area shape="rect" id="node10" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Scorer can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and Que..." alt="" coords="607,148,755,175"/><area shape="rect" id="node12" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;." alt="" coords="143,164,340,191"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1Aligner-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Cell.html">Cell</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">An <a class="el" href="classmoltk_1_1Aligner_1_1Cell.html" title="An Aligner::Cell is one node in the dynamic programming table.">Aligner::Cell</a> is one node in the dynamic programming table.  <a href="classmoltk_1_1Aligner_1_1Cell.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html">QueryPosition</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html" title="QueryPosition is an alignment column specialized to efficiently compute an alignment score with a Tar...">QueryPosition</a> is an alignment column specialized to efficiently compute an alignment score with a <a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html" title="TargetPosition is an alignment column specialized to efficiently compute an alignment score with a Qu...">TargetPosition</a>.  <a href="classmoltk_1_1Aligner_1_1QueryPosition.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html">Scorer</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html" title="Scorer can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and Que...">Scorer</a> can convert, in O(m+n) time, dumb sequence and structure residues into TargetPositions and QueryPositions, which can efficiently compute alignment scores.  <a href="classmoltk_1_1Aligner_1_1Scorer.html#details">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html">TargetPosition</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html" title="TargetPosition is an alignment column specialized to efficiently compute an alignment score with a Qu...">TargetPosition</a> is an alignment column specialized to efficiently compute an alignment score with a <a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html" title="QueryPosition is an alignment column specialized to efficiently compute an alignment score with a Tar...">QueryPosition</a>.  <a href="classmoltk_1_1Aligner_1_1TargetPosition.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b">TracebackPointer</a> { <br/>
&#160;&#160;<a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045">TRACEBACK_UP</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e">TRACEBACK_UPLEFT</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81">TRACEBACK_LEFT</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812">TRACEBACK_DONE</a>, 
<br/>
&#160;&#160;<a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220">TRACEBACK_NOT_INITIALIZED</a>
<br/>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">TracebackPointer help reconstruct the final alignment.  <a href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">Stage</a> { <br/>
&#160;&#160;<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a2877fdfe8fa9345c485dc69d2f5200ca">STAGE_EMPTY</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a42a9835d9845ffd8795ddcf578b20696">STAGE_SCORER</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a5ab4a5ba046f6d4b741e687baecbff92">STAGE_SEQUENCE</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208abbf7d1ed6268e8d3a7b8725a59b69d9f">STAGE_ALLOCATED</a>, 
<br/>
&#160;&#160;<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ad21d8375c870feed36071a180c7a797c">STAGE_TABLE_INITIALIZED</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208a22d74955c68c209611ee163f65aa2cc7">STAGE_RECURRENCE_COMPUTED</a>, 
<a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208ae27f4f916fb73fc17d2310072d718cb0">STAGE_TRACED</a>
<br/>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208" title="Aligner::Stage represents current state of an incomplete alignment.">Aligner::Stage</a> represents current state of an incomplete alignment.  <a href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">Information</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; <a class="el" href="classmoltk_1_1Aligner_1_1Cell.html">Cell</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; <a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">DpTable</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a99008604e446e2adc4f0df7e4afd6c9e">Aligner</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a9855904b20ecd75a1e44cfa955dd4f97">~Aligner</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align</a> (const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;, const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#aeb69db8c0ba583694b389d37e2f9f05b">get_end_gaps_free</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a1a3475cfc191d9c7efa26f26ba4436b8">set_end_gaps_free</a> (bool f)</td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html">Scorer</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a7d364467fa46629a81c3adbcc2cd2692">get_default_scorer</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classmoltk_1_1Aligner.html">Aligner</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a2a94cf962985576ec14640ee519fa371">get_shared_aligner</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Global shared aligner object used by <a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align()</a> method.  <a href="#a2a94cf962985576ec14640ee519fa371"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a5a7bc14266d9a09c00133aeee98ae039">init</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ae88d9a29786521dacbf511a8097bb063">allocate_dp_table</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a00167b2c4ea9d0e01e5ed56e8946b713">initialize_dp_table</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a47aa0cc272a3aa95d23dfec38d7883b0">initialize_dp_row</a> (size_t rowIndex, <a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a> &amp;row)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a66756b5e61b63ee8f26b6abb7b1de02e">compute_recurrence</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a38863ca0eb76e0241abedefaa69b0048">compute_cell_recurrence</a> (int i, int j)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a5c0dfb557f1fe73f8b0b6dc6eb029ab2">compute_cell_recurrence_freeE</a> (int i, int j)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ac1c097af307968d9caf76242977a288d">compute_cell_recurrence_freeF</a> (int i, int j)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a8d28c9bb018c6d4913e305c36093eeb0">compute_cell_recurrence_freeEF</a> (int i, int j)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ac6170833b8d8c742719e45186aff85b8">compute_traceback</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a729b4f44dd7e0411b0acdde5c1561af5">clear_positions</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ace84085990dcff6eac7f8baf8a5c5d9a">clear_scorer</a> ()</td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a401c10c0e6923397ba8227ef31137aca">b_local_aligner</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#afedcb89907a4037bccb3754a6e2eb2a3">m</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a3ee7cf4bee96c010e3644615f45f7dcc">n</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">DpTable</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a11e4f5632b62483c32b1169754f2261d">dp_table</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html">TargetPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a95bf66d275c37f120f9698a441eaa18b">seq1</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classmoltk_1_1Aligner_1_1QueryPosition.html">QueryPosition</a> * &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a934541c902699844d3fbcc4b04e96444">seq2</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html">Scorer</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">scorer</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#afc1bffe01773a0be7eba8a0961f75122">output_alignment</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#ac708decb0f2bc0a6c5563ee975f8e5a4">query_alignment</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Aligner.html#aa900f963fef40a9b258c93c32d7c2db1">target_alignment</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>The <a class="el" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a> class creates macromolecule sequence alignments and structure alignments. </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="a46c1b1a9807e0b189d8eee597df4d1fe"></a><!-- doxytag: member="moltk::Aligner::DpRow" ref="a46c1b1a9807e0b189d8eee597df4d1fe" args="" -->
<div class="memitem">
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          <td class="memname">typedef std::vector&lt;<a class="el" href="classmoltk_1_1Aligner_1_1Cell.html">Cell</a>&gt; <a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">moltk::Aligner::DpRow</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a8c586048912c20d16e8446694019f412"></a><!-- doxytag: member="moltk::Aligner::DpTable" ref="a8c586048912c20d16e8446694019f412" args="" -->
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          <td class="memname">typedef std::vector&lt;<a class="el" href="classmoltk_1_1Aligner.html#a46c1b1a9807e0b189d8eee597df4d1fe">DpRow</a>&gt; <a class="el" href="classmoltk_1_1Aligner.html#a8c586048912c20d16e8446694019f412">moltk::Aligner::DpTable</a></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
</div>
<a class="anchor" id="a22df03b2c1450636a9ab52e28976c2b3"></a><!-- doxytag: member="moltk::Aligner::Information" ref="a22df03b2c1450636a9ab52e28976c2b3" args="" -->
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          <td class="memname">typedef <a class="el" href="namespacemoltk_1_1units.html#a84d2541f1ab08c8ae38bea32fa7b33ca">moltk::units::Information</a> <a class="el" href="classmoltk_1_1Aligner.html#a22df03b2c1450636a9ab52e28976c2b3">moltk::Aligner::Information</a></td>
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</div>
</div>
<hr/><h2>Member Enumeration Documentation</h2>
<a class="anchor" id="a87bd8e86052f19040ae6de8de844f208"></a><!-- doxytag: member="moltk::Aligner::Stage" ref="a87bd8e86052f19040ae6de8de844f208" args="" -->
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          <td class="memname">enum <a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208">moltk::Aligner::Stage</a></td>
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<p><a class="el" href="classmoltk_1_1Aligner.html#a87bd8e86052f19040ae6de8de844f208" title="Aligner::Stage represents current state of an incomplete alignment.">Aligner::Stage</a> represents current state of an incomplete alignment. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208a2877fdfe8fa9345c485dc69d2f5200ca"></a><!-- doxytag: member="STAGE_EMPTY" ref="a87bd8e86052f19040ae6de8de844f208a2877fdfe8fa9345c485dc69d2f5200ca" args="" -->STAGE_EMPTY</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208a42a9835d9845ffd8795ddcf578b20696"></a><!-- doxytag: member="STAGE_SCORER" ref="a87bd8e86052f19040ae6de8de844f208a42a9835d9845ffd8795ddcf578b20696" args="" -->STAGE_SCORER</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208a5ab4a5ba046f6d4b741e687baecbff92"></a><!-- doxytag: member="STAGE_SEQUENCE" ref="a87bd8e86052f19040ae6de8de844f208a5ab4a5ba046f6d4b741e687baecbff92" args="" -->STAGE_SEQUENCE</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208abbf7d1ed6268e8d3a7b8725a59b69d9f"></a><!-- doxytag: member="STAGE_ALLOCATED" ref="a87bd8e86052f19040ae6de8de844f208abbf7d1ed6268e8d3a7b8725a59b69d9f" args="" -->STAGE_ALLOCATED</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208ad21d8375c870feed36071a180c7a797c"></a><!-- doxytag: member="STAGE_TABLE_INITIALIZED" ref="a87bd8e86052f19040ae6de8de844f208ad21d8375c870feed36071a180c7a797c" args="" -->STAGE_TABLE_INITIALIZED</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208a22d74955c68c209611ee163f65aa2cc7"></a><!-- doxytag: member="STAGE_RECURRENCE_COMPUTED" ref="a87bd8e86052f19040ae6de8de844f208a22d74955c68c209611ee163f65aa2cc7" args="" -->STAGE_RECURRENCE_COMPUTED</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="a87bd8e86052f19040ae6de8de844f208ae27f4f916fb73fc17d2310072d718cb0"></a><!-- doxytag: member="STAGE_TRACED" ref="a87bd8e86052f19040ae6de8de844f208ae27f4f916fb73fc17d2310072d718cb0" args="" -->STAGE_TRACED</em>&nbsp;</td><td>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55b"></a><!-- doxytag: member="moltk::Aligner::TracebackPointer" ref="adad98d3ee1780ac2f782bf87b466b55b" args="" -->
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          <td class="memname">enum <a class="el" href="classmoltk_1_1Aligner.html#adad98d3ee1780ac2f782bf87b466b55b">moltk::Aligner::TracebackPointer</a></td>
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<p>TracebackPointer help reconstruct the final alignment. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045"></a><!-- doxytag: member="TRACEBACK_UP" ref="adad98d3ee1780ac2f782bf87b466b55ba6da2cb4f6502904671847ec848503045" args="" -->TRACEBACK_UP</em>&nbsp;</td><td>
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<tr><td valign="top"><em><a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e"></a><!-- doxytag: member="TRACEBACK_UPLEFT" ref="adad98d3ee1780ac2f782bf87b466b55bae1838f55d1bd7835d79ffee07b42467e" args="" -->TRACEBACK_UPLEFT</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81"></a><!-- doxytag: member="TRACEBACK_LEFT" ref="adad98d3ee1780ac2f782bf87b466b55bab5353821ddae5b7ea5c6ce44d2d62d81" args="" -->TRACEBACK_LEFT</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812"></a><!-- doxytag: member="TRACEBACK_DONE" ref="adad98d3ee1780ac2f782bf87b466b55baed40c1c6e565bbbee48d601aaafe0812" args="" -->TRACEBACK_DONE</em>&nbsp;</td><td>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220"></a><!-- doxytag: member="TRACEBACK_NOT_INITIALIZED" ref="adad98d3ee1780ac2f782bf87b466b55ba4de2c99df6a5314ce86b8d850734d220" args="" -->TRACEBACK_NOT_INITIALIZED</em>&nbsp;</td><td>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="a99008604e446e2adc4f0df7e4afd6c9e"></a><!-- doxytag: member="moltk::Aligner::Aligner" ref="a99008604e446e2adc4f0df7e4afd6c9e" args="()" -->
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</div>
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<a class="anchor" id="a9855904b20ecd75a1e44cfa955dd4f97"></a><!-- doxytag: member="moltk::Aligner::~Aligner" ref="a9855904b20ecd75a1e44cfa955dd4f97" args="()" -->
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          <td class="memname">virtual moltk::Aligner::~Aligner </td>
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          <td><code> [virtual]</code></td>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a12bd197b84d50d7c1e8f952c91eb7666"></a><!-- doxytag: member="moltk::Aligner::align" ref="a12bd197b84d50d7c1e8f952c91eb7666" args="(const Alignment &amp;, const Alignment &amp;)" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> moltk::Aligner::align </td>
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          <td class="paramname">, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> &amp;&#160;</td>
          <td class="paramname">&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td></td>
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</div>
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<a class="anchor" id="ae88d9a29786521dacbf511a8097bb063"></a><!-- doxytag: member="moltk::Aligner::allocate_dp_table" ref="ae88d9a29786521dacbf511a8097bb063" args="()" -->
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          <td class="memname">void moltk::Aligner::allocate_dp_table </td>
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          <td><code> [protected]</code></td>
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<a class="anchor" id="a729b4f44dd7e0411b0acdde5c1561af5"></a><!-- doxytag: member="moltk::Aligner::clear_positions" ref="a729b4f44dd7e0411b0acdde5c1561af5" args="()" -->
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          <td class="memname">void moltk::Aligner::clear_positions </td>
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          <td><code> [protected]</code></td>
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</div>
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<a class="anchor" id="ace84085990dcff6eac7f8baf8a5c5d9a"></a><!-- doxytag: member="moltk::Aligner::clear_scorer" ref="ace84085990dcff6eac7f8baf8a5c5d9a" args="()" -->
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          <td class="memname">void moltk::Aligner::clear_scorer </td>
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          <td><code> [protected]</code></td>
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<a class="anchor" id="a38863ca0eb76e0241abedefaa69b0048"></a><!-- doxytag: member="moltk::Aligner::compute_cell_recurrence" ref="a38863ca0eb76e0241abedefaa69b0048" args="(int i, int j)" -->
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          <td class="memname">void moltk::Aligner::compute_cell_recurrence </td>
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          <td class="paramname"><em>j</em>&#160;</td>
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        <tr>
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<a class="anchor" id="a5c0dfb557f1fe73f8b0b6dc6eb029ab2"></a><!-- doxytag: member="moltk::Aligner::compute_cell_recurrence_freeE" ref="a5c0dfb557f1fe73f8b0b6dc6eb029ab2" args="(int i, int j)" -->
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          <td class="memname">void moltk::Aligner::compute_cell_recurrence_freeE </td>
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          <td class="paramname"><em>j</em>&#160;</td>
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<a class="anchor" id="a8d28c9bb018c6d4913e305c36093eeb0"></a><!-- doxytag: member="moltk::Aligner::compute_cell_recurrence_freeEF" ref="a8d28c9bb018c6d4913e305c36093eeb0" args="(int i, int j)" -->
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          <td class="paramname"><em>j</em>&#160;</td>
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<a class="anchor" id="ac1c097af307968d9caf76242977a288d"></a><!-- doxytag: member="moltk::Aligner::compute_cell_recurrence_freeF" ref="ac1c097af307968d9caf76242977a288d" args="(int i, int j)" -->
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          <td class="paramname"><em>j</em>&#160;</td>
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<a class="anchor" id="a66756b5e61b63ee8f26b6abb7b1de02e"></a><!-- doxytag: member="moltk::Aligner::compute_recurrence" ref="a66756b5e61b63ee8f26b6abb7b1de02e" args="()" -->
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          <td><code> [protected]</code></td>
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<a class="anchor" id="ac6170833b8d8c742719e45186aff85b8"></a><!-- doxytag: member="moltk::Aligner::compute_traceback" ref="ac6170833b8d8c742719e45186aff85b8" args="()" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> moltk::Aligner::compute_traceback </td>
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<a class="anchor" id="a7d364467fa46629a81c3adbcc2cd2692"></a><!-- doxytag: member="moltk::Aligner::get_default_scorer" ref="a7d364467fa46629a81c3adbcc2cd2692" args="()" -->
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          <td><code> [static]</code></td>
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<a class="anchor" id="aeb69db8c0ba583694b389d37e2f9f05b"></a><!-- doxytag: member="moltk::Aligner::get_end_gaps_free" ref="aeb69db8c0ba583694b389d37e2f9f05b" args="() const " -->
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<a class="anchor" id="a2a94cf962985576ec14640ee519fa371"></a><!-- doxytag: member="moltk::Aligner::get_shared_aligner" ref="a2a94cf962985576ec14640ee519fa371" args="()" -->
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          <td class="memname">static <a class="el" href="classmoltk_1_1Aligner.html">Aligner</a>&amp; moltk::Aligner::get_shared_aligner </td>
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          <td><code> [static]</code></td>
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<p>Global shared aligner object used by <a class="el" href="classmoltk_1_1Aligner.html#a12bd197b84d50d7c1e8f952c91eb7666">align()</a> method. </p>

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<a class="anchor" id="a5a7bc14266d9a09c00133aeee98ae039"></a><!-- doxytag: member="moltk::Aligner::init" ref="a5a7bc14266d9a09c00133aeee98ae039" args="()" -->
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          <td class="memname">void moltk::Aligner::init </td>
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          <td><code> [protected]</code></td>
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<a class="anchor" id="a47aa0cc272a3aa95d23dfec38d7883b0"></a><!-- doxytag: member="moltk::Aligner::initialize_dp_row" ref="a47aa0cc272a3aa95d23dfec38d7883b0" args="(size_t rowIndex, DpRow &amp;row)" -->
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        <tr>
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          <td>)</td>
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<a class="anchor" id="a00167b2c4ea9d0e01e5ed56e8946b713"></a><!-- doxytag: member="moltk::Aligner::initialize_dp_table" ref="a00167b2c4ea9d0e01e5ed56e8946b713" args="()" -->
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          <td class="memname">void moltk::Aligner::initialize_dp_table </td>
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          <td><code> [protected]</code></td>
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<a class="anchor" id="a1a3475cfc191d9c7efa26f26ba4436b8"></a><!-- doxytag: member="moltk::Aligner::set_end_gaps_free" ref="a1a3475cfc191d9c7efa26f26ba4436b8" args="(bool f)" -->
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          <td class="memname">void moltk::Aligner::set_end_gaps_free </td>
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          <td class="paramtype">bool&#160;</td>
          <td class="paramname"><em>f</em></td><td>)</td>
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<hr/><h2>Member Data Documentation</h2>
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<a class="anchor" id="afedcb89907a4037bccb3754a6e2eb2a3"></a><!-- doxytag: member="moltk::Aligner::m" ref="afedcb89907a4037bccb3754a6e2eb2a3" args="" -->
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<a class="anchor" id="a3ee7cf4bee96c010e3644615f45f7dcc"></a><!-- doxytag: member="moltk::Aligner::n" ref="a3ee7cf4bee96c010e3644615f45f7dcc" args="" -->
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          <td class="memname">size_t <a class="el" href="classmoltk_1_1Aligner.html#a3ee7cf4bee96c010e3644615f45f7dcc">moltk::Aligner::n</a><code> [protected]</code></td>
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<a class="anchor" id="afc1bffe01773a0be7eba8a0961f75122"></a><!-- doxytag: member="moltk::Aligner::output_alignment" ref="afc1bffe01773a0be7eba8a0961f75122" args="" -->
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<a class="anchor" id="ac708decb0f2bc0a6c5563ee975f8e5a4"></a><!-- doxytag: member="moltk::Aligner::query_alignment" ref="ac708decb0f2bc0a6c5563ee975f8e5a4" args="" -->
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<a class="anchor" id="a3ef4257103af46ae12c79b088e8343ae"></a><!-- doxytag: member="moltk::Aligner::scorer" ref="a3ef4257103af46ae12c79b088e8343ae" args="" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Aligner_1_1Scorer.html">Scorer</a>* <a class="el" href="classmoltk_1_1Aligner.html#a3ef4257103af46ae12c79b088e8343ae">moltk::Aligner::scorer</a><code> [protected]</code></td>
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<a class="anchor" id="a95bf66d275c37f120f9698a441eaa18b"></a><!-- doxytag: member="moltk::Aligner::seq1" ref="a95bf66d275c37f120f9698a441eaa18b" args="" -->
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          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1Aligner_1_1TargetPosition.html">TargetPosition</a>*&gt; <a class="el" href="classmoltk_1_1Aligner.html#a95bf66d275c37f120f9698a441eaa18b">moltk::Aligner::seq1</a><code> [protected]</code></td>
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<a class="anchor" id="a934541c902699844d3fbcc4b04e96444"></a><!-- doxytag: member="moltk::Aligner::seq2" ref="a934541c902699844d3fbcc4b04e96444" args="" -->
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<a class="anchor" id="aa900f963fef40a9b258c93c32d7c2db1"></a><!-- doxytag: member="moltk::Aligner::target_alignment" ref="aa900f963fef40a9b258c93c32d7c2db1" args="" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment.html">Alignment</a> <a class="el" href="classmoltk_1_1Aligner.html#aa900f963fef40a9b258c93c32d7c2db1">moltk::Aligner::target_alignment</a><code> [protected]</code></td>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Aligner_8hpp_source.html">Aligner.hpp</a></li>
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